Additional file 4 of Population structure, genetic diversity and pathotypes of Streptococcus suis isolated during the last 13 years from diseased pigs in Switzerland
Bibliographic record
Abstract
Additional file 4. Alignment of target gene sequences and the corresponding amino acid sequences used by pathotyping. Sequence alignment of copper ATPase 1-gene (A and B) and partial gene sequence alignment of type I RM system S protein-gene (C and D) of invasive disease-associated isolates of Swiss S. suis in comparison to the highly virulent reference strain P1/7 are shown visualizing different gene variants and its corresponding protein sequences. Conserved, matching nucleotide residues are illustrated as blue dots, whereas red represents differences of nucleotide sequences. (A) Copper ATPase 1-gene sequences of S. suis PP463 (cps2, ST28), SS470 (cps1/2, ST28), PP423 (cps1/2, ST1133), and PP536 (cps9, ST1105) are represented. Primer sequences of the pathotyping tool are indicated in green. A duplication of a 54 bp long DNA segment in isolate SS470 and deletion of a 21 bp fragment in all represented Swiss isolates could be observed, illustrating a high genetic variability. (B) Corresponding amino acid sequence alignment of Copper ATPase 1 is shown. (C) RM system S protein gene sequences of S. suis PP463 (cps2, ST28), PP423 (cps1/2, ST1133), and PP269 (cps1, ST13) are represented. The forward primer is indicated in green, whereas the reverse primer could not be shown since illustrated Swiss isolates are truncated. (D) Corresponding amino acid sequence alignment of RM systems S protein is shown.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.019 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.838 | 0.082 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".